NPASS Compound

Natural Product: NPC300419

Natural Product ID	NPC300419
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	Polygalasaponin E
IUPAC Name	(2S,3R,4S,4aR,6aR,6bS,8aS,12aS,14aR,14bR)-8a-[(2S,3R,4S,5S,6R)-3-[(2S,3R,4S,5R,6S)-3,4-dihydroxy-6-methyl-5-[(2S,3R,4S,5R)-3,4,5-trihydroxyoxan-2-yl]oxyoxan-2-yl]oxy-4,5-dihydroxy-6-(hydroxymethyl)oxan-2-yl]oxycarbonyl-2,3-dihydroxy-4,6a,6b,11,11,14b-hexamethyl-1,2,3,4a,5,6,7,8,9,10,12,12a,14,14a-tetradecahydropicene-4-carboxylic acid
Synonyms	polygalasaponin E
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	CHEMBL503227
PubChem CID	11571566
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000259] Prenol lipids [CHEMONTID:0002049] Terpene glycosides [CHEMONTID:0001580] Triterpene glycosides [CHEMONTID:0002358] Triterpene saponins

The Chemical Classification was calculated by Classyfire, a software for chemical taxonomy calculation. Reference: DOI:10.1186/s13321-016-0174-y.

Chemical Representations

RDKit 3D 140147 0 0 0 0 0 0 0 0999 V2000 1.7272 -6.2397 -4.4781 O 0 0 0 0 0 0 0 0 0 0 0 0 2.8396 -6.2006 -3.6383 C 0 0 0 0 0 0 0 0 0 0 0 0 3.2637 -4.7837 -3.3294 C 0 0 1 0 0 0 0 0 0 0 0 0 2.1976 -4.1476 -2.7103 O 0 0 0 0 0 0 0 0 0 0 0 0 2.4831 -2.7651 -2.5521 C 0 0 1 0 0 0 0 0 0 0 0 0 1.2310 -2.2033 -2.2557 O 0 0 0 0 0 0 0 0 0 0 0 0 0.4967 -1.5189 -3.2533 C 0 0 0 0 0 0 0 0 0 0 0 0 1.0127 -1.4530 -4.3425 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.8398 -0.9737 -2.8021 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.5365 -2.2138 -2.2964 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.4651 -2.1275 -1.1686 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.9511 -0.7864 -0.7709 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.8868 0.2658 -0.9438 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.0844 1.4093 -0.3089 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.2246 1.7682 0.5451 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.0649 0.5934 0.8359 C 0 0 1 0 0 0 0 0 0 0 0 0 -3.3300 -0.7086 0.6987 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.0080 -0.6823 1.4680 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.0924 -1.8928 1.1614 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.3008 -1.7086 1.9744 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.9234 -0.3571 2.0131 C 0 0 2 0 0 0 0 0 0 0 0 0 -4.9029 0.7021 2.1165 C 0 0 1 0 0 0 0 0 0 0 0 0 -4.0818 0.7441 3.3426 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.5984 2.0565 1.9735 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.8216 2.2424 2.7726 C 0 0 1 0 0 0 0 0 0 0 0 0 -7.4117 1.0838 3.4729 C 0 0 1 0 0 0 0 0 0 0 0 0 -7.0519 -0.2695 2.9989 C 0 0 2 0 0 0 0 0 0 0 0 0 -6.7394 -1.1304 4.2213 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.2910 -0.9123 2.4192 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.2394 -1.3951 1.2698 O 0 0 0 0 0 0 0 0 0 0 0 0 -9.4637 -0.9780 3.1224 O 0 0 0 0 0 0 0 0 0 0 0 0 -7.2533 1.1714 4.8845 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.6591 3.2594 3.7480 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.6757 0.0499 -1.7296 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.0256 1.2705 -2.2874 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.6507 1.7860 -3.5376 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.6989 0.6959 -4.6146 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.4788 -0.4557 -4.0710 C 0 0 0 0 0 0 0 0 0 0 0 0 0.3266 2.8270 -4.1191 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.9508 2.4890 -3.4041 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.1865 -0.4719 -1.5905 C 0 0 0 0 0 0 0 0 0 0 0 0 3.6030 -2.5186 -1.6508 C 0 0 1 0 0 0 0 0 0 0 0 0 4.4824 -3.7315 -1.3800 C 0 0 2 0 0 0 0 0 0 0 0 0 4.4099 -4.8225 -2.3761 C 0 0 2 0 0 0 0 0 0 0 0 0 5.6051 -4.9112 -3.1372 O 0 0 0 0 0 0 0 0 0 0 0 0 4.1920 -4.2913 -0.1083 O 0 0 0 0 0 0 0 0 0 0 0 0 4.3650 -1.4145 -2.0147 O 0 0 0 0 0 0 0 0 0 0 0 0 4.5703 -0.4628 -1.0815 C 0 0 2 0 0 0 0 0 0 0 0 0 3.9723 0.7373 -1.4878 O 0 0 0 0 0 0 0 0 0 0 0 0 3.8184 1.6536 -0.4594 C 0 0 1 0 0 0 0 0 0 0 0 0 2.7177 1.2899 0.4796 C 0 0 0 0 0 0 0 0 0 0 0 0 5.1589 1.7801 0.2683 C 0 0 1 0 0 0 0 0 0 0 0 0 6.2061 1.3733 -0.7269 C 0 0 2 0 0 0 0 0 0 0 0 0 6.0481 -0.1577 -0.8545 C 0 0 1 0 0 0 0 0 0 0 0 0 6.5159 -0.6745 0.3564 O 0 0 0 0 0 0 0 0 0 0 0 0 7.4964 1.5953 -0.2666 O 0 0 0 0 0 0 0 0 0 0 0 0 5.2731 3.0422 0.7886 O 0 0 0 0 0 0 0 0 0 0 0 0 5.4120 3.0686 2.1572 C 0 0 2 0 0 0 0 0 0 0 0 0 4.2808 3.5797 2.8116 O 0 0 0 0 0 0 0 0 0 0 0 0 4.2911 3.2471 4.1369 C 0 0 0 0 0 0 0 0 0 0 0 0 5.5605 2.7716 4.7375 C 0 0 2 0 0 0 0 0 0 0 0 0 6.7946 3.3684 4.1567 C 0 0 1 0 0 0 0 0 0 0 0 0 6.5998 3.7875 2.6954 C 0 0 1 0 0 0 0 0 0 0 0 0 7.7880 3.5573 2.0246 O 0 0 0 0 0 0 0 0 0 0 0 0 7.2308 4.4456 4.9228 O 0 0 0 0 0 0 0 0 0 0 0 0 5.6632 1.3763 4.7650 O 0 0 0 0 0 0 0 0 0 0 0 0 1.9937 -6.3994 -5.4273 H 0 0 0 0 0 0 0 0 0 0 0 0 3.7254 -6.6964 -4.1338 H 0 0 0 0 0 0 0 0 0 0 0 0 2.6478 -6.7725 -2.7118 H 0 0 0 0 0 0 0 0 0 0 0 0 3.5171 -4.3171 -4.3077 H 0 0 0 0 0 0 0 0 0 0 0 0 2.7237 -2.4678 -3.6201 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.7233 -2.9801 -2.0994 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.0281 -2.6599 -3.2191 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.3544 -2.7861 -1.4296 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.0167 -2.6461 -0.2978 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.3259 2.2099 -0.4029 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.8672 2.5193 -0.0109 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.9072 2.3606 1.4433 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.8843 0.5663 0.0521 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.7585 0.3089 1.8548 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.0171 -1.4616 2.2911 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.1708 -1.0114 0.8236 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.3304 -2.5119 0.2436 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.4169 -2.6033 1.7401 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.1673 -2.1492 2.9941 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.1124 -2.3868 1.5381 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.4216 -0.2239 1.0036 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.5441 -0.1879 3.5820 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.2844 1.5251 3.2294 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.6249 1.0602 4.2536 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.7254 2.3194 0.8911 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.8329 2.8068 2.3297 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.5937 2.6885 2.0603 H 0 0 0 0 0 0 0 0 0 0 0 0 -8.5401 1.2022 3.3840 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.0865 -2.1770 4.0764 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.7267 -1.0310 4.5924 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.4015 -0.7362 5.0450 H 0 0 0 0 0 0 0 0 0 0 0 0 -10.0964 -1.7651 3.0686 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.7673 1.9407 5.2439 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.0360 4.1218 3.4530 H 0 0 0 0 0 0 0 0 0 0 0 0 0.1010 -0.3963 -1.0318 H 0 0 0 0 0 0 0 0 0 0 0 0 0.2176 2.0780 -1.6189 H 0 0 0 0 0 0 0 0 0 0 0 0 1.0046 0.9122 -2.6302 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.3128 1.1561 -5.4408 H 0 0 0 0 0 0 0 0 0 0 0 0 0.3166 0.5069 -4.9308 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.4904 -1.2947 -4.8007 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.5025 -0.0560 -3.8938 H 0 0 0 0 0 0 0 0 0 0 0 0 0.3333 3.7393 -3.5111 H 0 0 0 0 0 0 0 0 0 0 0 0 1.3316 2.3678 -4.0494 H 0 0 0 0 0 0 0 0 0 0 0 0 0.1298 2.9796 -5.2014 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.8150 1.8425 -3.2183 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.8719 3.2085 -2.5617 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.1060 3.1134 -4.3153 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.3069 0.5588 -1.8836 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.0746 -1.0639 -2.5580 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.0942 -0.9573 -1.1469 H 0 0 0 0 0 0 0 0 0 0 0 0 3.2294 -2.2673 -0.6336 H 0 0 0 0 0 0 0 0 0 0 0 0 5.5561 -3.4075 -1.2806 H 0 0 0 0 0 0 0 0 0 0 0 0 4.3596 -5.8346 -1.8634 H 0 0 0 0 0 0 0 0 0 0 0 0 6.2557 -5.4189 -2.5911 H 0 0 0 0 0 0 0 0 0 0 0 0 3.4207 -3.8429 0.3192 H 0 0 0 0 0 0 0 0 0 0 0 0 4.1363 -0.6682 -0.0831 H 0 0 0 0 0 0 0 0 0 0 0 0 3.6213 2.6335 -0.9151 H 0 0 0 0 0 0 0 0 0 0 0 0 2.2144 2.2313 0.8361 H 0 0 0 0 0 0 0 0 0 0 0 0 1.9476 0.7222 -0.0772 H 0 0 0 0 0 0 0 0 0 0 0 0 3.0673 0.7100 1.3611 H 0 0 0 0 0 0 0 0 0 0 0 0 5.2011 1.0526 1.1090 H 0 0 0 0 0 0 0 0 0 0 0 0 6.0642 1.8291 -1.7290 H 0 0 0 0 0 0 0 0 0 0 0 0 6.6869 -0.4510 -1.7056 H 0 0 0 0 0 0 0 0 0 0 0 0 7.3530 -1.1988 0.2307 H 0 0 0 0 0 0 0 0 0 0 0 0 8.1582 0.9666 -0.6726 H 0 0 0 0 0 0 0 0 0 0 0 0 5.4630 1.9922 2.5026 H 0 0 0 0 0 0 0 0 0 0 0 0 3.9201 4.1601 4.6962 H 0 0 0 0 0 0 0 0 0 0 0 0 3.5097 2.4588 4.3719 H 0 0 0 0 0 0 0 0 0 0 0 0 5.5604 3.0588 5.8349 H 0 0 0 0 0 0 0 0 0 0 0 0 7.6238 2.6155 4.1887 H 0 0 0 0 0 0 0 0 0 0 0 0 6.4559 4.8910 2.7401 H 0 0 0 0 0 0 0 0 0 0 0 0 8.1170 4.3431 1.5163 H 0 0 0 0 0 0 0 0 0 0 0 0 8.0162 4.2083 5.4806 H 0 0 0 0 0 0 0 0 0 0 0 0 6.6119 1.1342 4.5607 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 2 3 1 0 3 4 1 0 4 5 1 0 5 6 1 0 6 7 1 0 7 8 2 0 9 7 1 6 9 10 1 0 10 11 1 0 11 12 1 0 12 13 1 0 13 14 2 0 14 15 1 0 15 16 1 0 16 17 1 0 17 18 1 1 17 19 1 0 19 20 1 0 20 21 1 0 21 22 1 0 22 23 1 1 22 24 1 0 24 25 1 0 25 26 1 0 26 27 1 0 27 28 1 1 27 29 1 0 29 30 2 0 29 31 1 0 26 32 1 0 25 33 1 0 13 34 1 0 34 35 1 0 35 36 1 0 36 37 1 0 37 38 1 0 36 39 1 0 36 40 1 0 12 41 1 6 5 42 1 0 42 43 1 0 43 44 1 0 44 45 1 0 43 46 1 0 42 47 1 0 47 48 1 0 48 49 1 0 49 50 1 0 50 51 1 0 50 52 1 0 52 53 1 0 53 54 1 0 54 55 1 0 53 56 1 0 52 57 1 0 57 58 1 0 58 59 1 0 59 60 1 0 60 61 1 0 61 62 1 0 62 63 1 0 63 64 1 0 62 65 1 0 61 66 1 0 44 3 1 0 54 48 1 0 63 58 1 0 38 9 1 0 34 9 1 0 17 12 1 0 27 21 1 0 22 16 1 0 1 67 1 0 2 68 1 0 2 69 1 0 3 70 1 6 5 71 1 6 10 72 1 0 10 73 1 0 11 74 1 0 11 75 1 0 14 76 1 0 15 77 1 0 15 78 1 0 16 79 1 6 18 80 1 0 18 81 1 0 18 82 1 0 19 83 1 0 19 84 1 0 20 85 1 0 20 86 1 0 21 87 1 6 23 88 1 0 23 89 1 0 23 90 1 0 24 91 1 0 24 92 1 0 25 93 1 6 26 94 1 1 28 95 1 0 28 96 1 0 28 97 1 0 31 98 1 0 32 99 1 0 33100 1 0 34101 1 1 35102 1 0 35103 1 0 37104 1 0 37105 1 0 38106 1 0 38107 1 0 39108 1 0 39109 1 0 39110 1 0 40111 1 0 40112 1 0 40113 1 0 41114 1 0 41115 1 0 41116 1 0 42117 1 1 43118 1 1 44119 1 1 45120 1 0 46121 1 0 48122 1 1 50123 1 6 51124 1 0 51125 1 0 51126 1 0 52127 1 1 53128 1 6 54129 1 6 55130 1 0 56131 1 0 58132 1 1 60133 1 0 60134 1 0 61135 1 1 62136 1 6 63137 1 1 64138 1 0 65139 1 0 66140 1 0 M END

Standard InCHIKey	AWUKSVPVFAMJKF-UCOQPZAKSA-N
Standard InCHI	InChI=1S/C47H74O19/c1-20-34(64-37-32(55)28(51)24(50)19-61-37)31(54)33(56)38(62-20)65-35-30(53)29(52)25(18-48)63-39(35)66-41(60)47-14-12-42(2,3)16-22(47)21-8-9-26-43(4)17-23(49)36(57)46(7,40(58)59)27(43)10-11-45(26,6)44(21,5)13-15-47/h8,20,22-39,48-57H,9-19H2,1-7H3,(H,58,59)/t20-,22-,23-,24+,25+,26+,27+,28-,29+,30-,31-,32+,33+,34-,35+,36-,37-,38-,39-,43+,44+,45+,46-,47-/m0/s1
SMILES	OC[C@H]1O[C@@H](OC(=O)[C@]23CC[C@@]4(C(=CC[C@H]5[C@@]4(C)CC[C@@H]4[C@]5(C)C[C@@H]([C@@H]([C@@]4(C)C(=O)O)O)O)[C@@H]3CC(CC2)(C)C)C)[C@@H]([C@H]([C@@H]1O)O)O[C@@H]1O[C@@H](C)[C@@H]([C@H]([C@H]1O)O)O[C@@H]1OC[C@H]([C@@H]([C@H]1O)O)O

Calculated Properties

Physi-Chem Properties

Molecular Weight:	942.48	Volume:	912.121 ? Van der Waals volume.
Dense:	1.033	LogP:	1.025 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	1.905 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-3.648 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	9.0	Rigid Bonds:	46.0
TPSA:	312.05 ? Topological Polar Surface Area.	H-Bond Acceptor:	19.0
H-Bond Donor:	11.0	Rings:	8.0
Heavy Atoms:	19.0

MedChem Properties

QED Drug-Likeness Score:	0.111	GASA:	1.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	6.426	Fsp³:	0.915
MCE-18:	177.778 ? MCE-18 stands for medicinal chemistry evolution.MCE-18≥45 is considered a suitable value.	Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Rejected	GSK Rule:	Accepted
Golden Triangle Rule:	Accepted	BMS Rule:	1
Chelating Alert:	0	PAINS Alert:	0
Colloidal aggregators:	0.714	Fluc inhibitor:	0.0 ? The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:	0.009 ? The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1	Green fluorescence:	0.001 ? The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:	0.184	Promiscuous compounds:	0.231

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-6.389	MDCK Permeability:	-5.075
Pgp-inhibitor:	0.0	Pgp-substrate:	0.284
PAMPA:	1.0 ? The experimental data for Peff was logarithmically transformed (logPeff). Molecules with log Peff values below 2.0 were classified as low-permeability (Category 0), while those with log Peff values exceeding 2.5 were classified as high-permeability (Category 1).	Human Intestinal Absorption (HIA):	0.934
20% Bioavailability (F20%):	0.878	30% Bioavailability (F30%):	0.999
50% Bioavailability (F50%):	1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.005	MRP1:	0.236
Plasma Protein Binding (PPB):	73.674%	Volume Distribution (VD):	-0.343
Fu:	14.663% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	1.0
OATP1B3 inhibitor:	1.0	BCRP inhibitor:	0.0
BSEP inhibitor:	0.0

ADMET: Metabolism

CYP1A2-inhibitor:	0.0	CYP1A2-substrate:	0.0
CYP2C19-inhibitor:	0.0	CYP2C19-substrate:	0.001
CYP2C9-inhibitor:	0.0	CYP2C9-substrate:	0.0
CYP2D6-inhibitor:	0.0	CYP2D6-substrate:	0.0
CYP3A4-inhibitor:	0.0	CYP3A4-substrate:	0.001
CYP2B6-substrate:	0.0	CYP2C8-inhibitor:	0.073
HLM stability:	0.682 ? Human liver microsomal (HLM) stability. Category 0: stable+ (HLM > 30 min); Category 1: unstable- (HLM ≤ 30 min). The output value is the probability of human liver microsomal instability, where a value closer to 1 indicates a higher likelihood of instability.

ADMET: Excretion

Clearance (CL):

-0.104

Half-life (T1/2):

3.582

ADMET: Toxicity

hERG Blockers:	0.001	hERG Blockers (10um):	0.001
Human Hepatotoxicity (H-HT):	0.691	Drug-induced Liver Injury (DILI):	0.789
AMES Toxicity:	0.711	Rat Oral Acute Toxicity:	0.005
Maximum Recommended Daily Dose:	0.003	Skin Sensitization:	1.0
Carcinogencity:	0.067	Eye Corrosion:	0.0
Eye Irritation:	0.0	Respiratory Toxicity:	0.007
Drug-induced Neurotoxicity:	0.0	Ototoxicity:	0.998
Hematotoxicity:	0.677	Drug-induced Nephrotoxicity:	0.998
Genotoxicity:	0.461	RPMI-8226 Immunitoxicity:	0.164
A549 Cytotoxicity:	0.469	Hek293 Cytotoxicity:	0.053
BCF:	0.784 ? Bioconcentration factors are used for considering secondary poisoning potential and assessing risks to human health via the food chain. The unit is -log10[(mg/L)/(1000*MW)].	IGC50:	3.655 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	5.54 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	4.412 ? 96 hour fathead minnow LC50. The unit of LC50FM is -log10[(mg/L)/(1000*MW)].

Species Source

Organism ID	Organism Name	Taxonomy Level	Family	SuperKingdom	Isolation Part	Collection Location	Collection Time	Reference
NPO11905	Polygala japonica	Species	Polygalaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[16643032]
NPO11905	Polygala japonica	Species	Polygalaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO11905	Polygala japonica	Species	Polygalaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO11905	Polygala japonica	Species	Polygalaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]

Note for Reference:
In addition to directly collecting NP source organism data from primary literature (where reference will provided as NCBI PMID or DOI links), NPASS also integrated them from below databases:
☉ UNPD: Universal Natural Products Database [PMID: 23638153].
☉ StreptomeDB: a database of streptomycetes natural products [PMID: 33051671].
☉ TM-MC: a database of medicinal materials and chemical compounds in Northeast Asian traditional medicine [PMID: 26156871].
☉ TCM@Taiwan: a Traditional Chinese Medicine database [PMID: 21253603].
☉ TCMID: a Traditional Chinese Medicine database [PMID: 29106634].
☉ TCMSP: The traditional Chinese medicine systems pharmacology database and analysis platform [PMID: 24735618].
☉ HerDing: a herb recommendation system to treat diseases using genes and chemicals [PMID: 26980517].
☉ MetaboLights: a metabolomics database [PMID: 27010336].
☉ FooDB: a database of constituents, chemistry and biology of food species [www.foodb.ca].

NP Quantity Composition/Concentration

Organism ID	Organism Name	Organism Material Preparation	Organism Part	NP Quantity (Standard)	NP Quantity (Minimum)	NP Quantity (Maximum)	Quantity Unit	Reference

Note for Reference:
In addition to directly collecting NP quantitative data from primary literature (where reference will provided as NCBI PMID or DOI links), NPASS also integrated NP quantitative records for specific NP domains (e.g., NPS from foods or herbs) from domain-specific databases. These databases include:
☉ DUKE: Dr. Duke's Phytochemical and Ethnobotanical Databases.
☉ PHENOL EXPLORER: is the first comprehensive database on polyphenol content in foods [PMID: 24103452], its homepage can be accessed at here.
☉ FooDB: a database of constituents, chemistry and biology of food species [www.foodb.ca].

Biological Activity

Activity Type	# Activity
Activity	2

Activity Type	# Activity
Organism	2

Molecular-level activity

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference

In vitro activity

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference

In vivo activity

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT32	Organism	Mus musculus	Mus musculus	Activity	=	35.4	%	PubChem BioAssay data set
NPT32	Organism	Mus musculus	Mus musculus	Activity	=	58.1	%	PubChem BioAssay data set

Experimental ADME

Experiment Model	Experiment Tissue	ADME Type	ADME Relation	ADME Value	ADME Unit	Reference

Experimental Toxicity

Quantitative toxicity

Experiment Model	Experiment Organism	Toxicity Type	Toxicity Relation	Toxicity Value	Toxicity Unit	Reference

Common Abbreviations:
LC: Lethal Concentration; LD: Lethal Dose; LT:Lethal Time; NOAEL: No-observed-adverse-effect Level; BMDL: Benchmark Dose Lower Confidence Limit; BMD: Benchmark Dose; BMC:Benchmark Concentration; LOAEL: Lowest Observed Adverse Effect Level; RfD:Reference Dose; RfC:Reference Concentration; MRL: Minimal Risk Level; MEG: Maximum Exposure Guideline; PAC: Protective Action Criteria

Categorical toxicity labels

Hepatotoxicity	Carcinogenicity	Mutagenicity	Cardiotoxicity	Respiratory Toxicity	Eye Irritation	Endocrine Disruption

Note for Reference:
In addition to directly collecting NP quantitative data from primary literature (where reference will provided as NCBI PMID or DOI links), NPASS also integrated NP toxicity records from domain-specific databases. These databases include:
☉ ToxValDB: a curated database that compiles quantitative toxicity values for chemicals from diverse public sources to support toxicological research and risk assessment.
☉ TOXRIC: a comprehensive, free-to-access, online database providing toxicological/feature data. The toxicity labels are retrieved from this database. [PMID: 36400569]

Chemically structural similarity

Similar Active Natural Products in NPASS

Top-200 similar NPs were calculated against the active-NP-set (includes approximately 50,000 NPs with experimentally-derived bioactivity available in NPASS)

Similarity is measured using the Tanimoto coefficient (Tc) , which compares the binary fingerprints of two molecules. Tc is calculated as the intersection divided by the union of '1' bits in the fingerprints, ranging from 0 to 1, with 1 indicating highest similarity.

● The left chart: Distribution of similarity level between NPC300419 and all remaining natural products in the NPASS database.
● The right table: Most similar natural products (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	22555
0.1-0.2	23189
0.2-0.3	3021
0.3-0.4	658
0.4-0.5	333
0.5-0.6	86
0.6-0.7	8
0.7-0.8	0
0.8-0.85	1
0.85-0.9	0
0.9-0.95	0
0.95-1	0

Similarity Score	Similarity Level	Natural Product ID
0.8378	Intermediate Similarity	NPC473645
0.6535	Remote Similarity	NPC478823
0.6393	Remote Similarity	NPC191827
0.6328	Remote Similarity	NPC70809
0.6195	Remote Similarity	NPC469946
0.6167	Remote Similarity	NPC75287
0.6111	Remote Similarity	NPC57484
0.605	Remote Similarity	NPC301449
0.605	Remote Similarity	NPC601290
0.5984	Remote Similarity	NPC484943
0.594	Remote Similarity	NPC478825
0.5917	Remote Similarity	NPC481079
0.5902	Remote Similarity	NPC815
0.582	Remote Similarity	NPC104137
0.582	Remote Similarity	NPC26626
0.582	Remote Similarity	NPC187290
0.5818	Remote Similarity	NPC209894
0.5798	Remote Similarity	NPC609763
0.5794	Remote Similarity	NPC480419
0.5789	Remote Similarity	NPC478824
0.5769	Remote Similarity	NPC470876
0.5725	Remote Similarity	NPC478822
0.5667	Remote Similarity	NPC297263
0.563	Remote Similarity	NPC251768
0.5565	Remote Similarity	NPC31838
0.5556	Remote Similarity	NPC224381
0.553	Remote Similarity	NPC484942
0.5461	Remote Similarity	NPC475368
0.5448	Remote Similarity	NPC135849
0.5424	Remote Similarity	NPC295371
0.542	Remote Similarity	NPC487505
0.542	Remote Similarity	NPC85154
0.5414	Remote Similarity	NPC258617
0.5391	Remote Similarity	NPC123522
0.536	Remote Similarity	NPC295823
0.536	Remote Similarity	NPC174720
0.536	Remote Similarity	NPC241909
0.536	Remote Similarity	NPC475467
0.5357	Remote Similarity	NPC477464
0.5338	Remote Similarity	NPC473452
0.5338	Remote Similarity	NPC480418
0.5338	Remote Similarity	NPC286457
0.5333	Remote Similarity	NPC192791
0.5333	Remote Similarity	NPC112352
0.5333	Remote Similarity	NPC477463
0.5328	Remote Similarity	NPC475591
0.5328	Remote Similarity	NPC63159
0.5328	Remote Similarity	NPC236870
0.5317	Remote Similarity	NPC481078
0.5308	Remote Similarity	NPC257211
0.5308	Remote Similarity	NPC135904
0.5294	Remote Similarity	NPC488561
0.5274	Remote Similarity	NPC472268
0.5238	Remote Similarity	NPC96641
0.5238	Remote Similarity	NPC163183
0.5231	Remote Similarity	NPC475899
0.5227	Remote Similarity	NPC471577
0.5225	Remote Similarity	NPC199457
0.5205	Remote Similarity	NPC297950
0.5194	Remote Similarity	NPC60557
0.5194	Remote Similarity	NPC76972
0.5194	Remote Similarity	NPC469782
0.5194	Remote Similarity	NPC67857
0.5194	Remote Similarity	NPC204414
0.5188	Remote Similarity	NPC481080
0.518	Remote Similarity	NPC250247
0.5161	Remote Similarity	NPC222580
0.5152	Remote Similarity	NPC470218
0.5149	Remote Similarity	NPC473386
0.5135	Remote Similarity	NPC237503
0.5128	Remote Similarity	NPC29069
0.5126	Remote Similarity	NPC235405
0.5126	Remote Similarity	NPC139894
0.5122	Remote Similarity	NPC480475
0.5109	Remote Similarity	NPC202828
0.5109	Remote Similarity	NPC119592
0.5109	Remote Similarity	NPC236638
0.5109	Remote Similarity	NPC294453
0.5091	Remote Similarity	NPC167383
0.5085	Remote Similarity	NPC48499
0.5083	Remote Similarity	NPC249848
0.5083	Remote Similarity	NPC107966
0.5081	Remote Similarity	NPC235438
0.5079	Remote Similarity	NPC281148
0.5077	Remote Similarity	NPC475287
0.5076	Remote Similarity	NPC123199
0.5074	Remote Similarity	NPC471580
0.5074	Remote Similarity	NPC41061
0.5074	Remote Similarity	NPC227551
0.5072	Remote Similarity	NPC37860
0.5044	Remote Similarity	NPC68419
0.5043	Remote Similarity	NPC90856
0.5041	Remote Similarity	NPC104071
0.5038	Remote Similarity	NPC283417
0.5038	Remote Similarity	NPC200049

Similar Clinical/Approved Drugs

Similarity level is defined by Tanimoto coefficient (Tc) between two molecules.

● The left chart: Distribution of similarity level between NPC300419 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	6667
0.1-0.2	2428
0.2-0.3	51
0.3-0.4	4
0.4-0.5	0
0.5-0.6	0
0.6-0.7	0
0.7-0.8	0
0.8-0.85	0
0.85-0.9	0
0.9-0.95	0
0.95-1	0

Similarity Score	Similarity Level	Drug ID	Developmental Stage
		NPD

Bioactivity similarity

Similar Natural Products in NPASS

Similarity level is defined by Bioactivity similarity was calculated based on bioactivity descriptors of compounds. The bioactivity descriptors were calculated by a recently developed AI algorithm Chemical Checker (CC) [Nature Biotechnology, 38:1087–1096, 2020; Nature Communications, 12:3932, 2021], which evaluated bioactivity similarities at five levels:
☉ A: chemistry similarity;
☉ B: biological targets similarity;
☉ C: networks similarity;
☉ D: cell-based bioactivity similarity;
☉ E: similarity based on clinical data.
Those 5 categories of CC bioactivity descriptors were calculated and then subjected to manifold projection using UMAP algorithm, to project all NPs on a 2-Dimensional space. The current NP was highlighted with a small circle in the 2-D map. Below figures: left-to-right, A-to-E.

A: chemistry similarity

B: biological targets similarity

C: networks similarity

D: cell-based bioactivity similarity

E: similarity based on clinical data